Bioreactor and bioprocessing technique

ABSTRACT

The inventive bioprocessing system (and technique) relies on non-invasive optical chemical sensing technology wherein an optical excitation source excites an optical chemical sensor. The optical chemical sensor then emits luminescence or absorbs light which is measured by a detector. The luminescence emitted from the chemical sensor or the amount of light absorbed by the chemical sensor is related to the concentration of an analyte, such as oxygen. If the luminescence emitted changes, or if the amount of light absorbed changes, then the concentration of the analyte has changed. Using such a system to measure and adjust multiple parameters at one time allows one to efficiently and cost-effectively determine optimal conditions for a given cell type and/or cell environment, for example. By combining cell cultivation with optical chemical sensing technology, cultivation can be successfully and rapidly performed, controlled and monitored in small volumes in an automated, parallel fashion at less expense than current bioprocess techniques.

[0001] This application claims priority to U.S. Provisional ApplicationSerial No. 60/225,108, filed Aug. 14, 2000, whose entire disclosure isincorporated herein by reference.

BACKGROUND OF THE INVENTION

[0002] 1. Field of the Invention

[0003] The present invention pertains to a bioreactor, moreparticularly, a low volume bioreactor (microbioreactor). Further, thepresent invention pertains to the use of non-invasive optical chemicalsensors to measure multiple parameters in a bioprocessing system.

[0004] 2. Background of Related Art

[0005] Bioprocesses are important in a wide variety of industries suchas pharmaceutical, food, ecology and water treatment, as well as toventures such as the human genome project (Arroyo, M. et al, BiotechnolProg. 16: 368- 371 (2000); Bakoyianis, V. and Koutinas, A. A.,Biotechnol Bioeng. 49: 197-203 (1996); Bylund, F. et al, BiotechnolBioeng. 69:119-128 (2000); Handa-Corrigan, A. et al., J. Chem. Technol.Biotechnol. 71: 51-56 (1998); López-López, A. et al., Biotechnol Bioeng.63: 79-86 (1999); McIntyre, J. J. et al., Biotechnol Bioeng. 62: 576-582(1999); Pressman, J. G. et al., Biotechnol Bioeng. 62: 681-692 (1999);Yang, J.-D. et al., Biotechnol Bioeng. 69: 74-82 (2000)).

[0006] The sequencing of the human genome has been a mammoth task,however, many have pointed out that this effort pales in comparison towhat lies ahead. The next step is to identify what turns the identifiedgenes on and what proteins these genes express. Cell cultivation willplay a critical role in elucidating these factors. More specifically,after the 50,000-100,000 human genes are cloned into various hosts, suchas bacteria, yeast and tissue culture cells, an enormous permutation ofculture conditions will have to be evaluated to identify the criticalfactors that turn the genes on. Next, the identity of the proteinsproduced will have to be determined, thus, efficient productionstrategies will be needed to obtain enough proteins for crystallographicstudies. A highly combinatorial technique could significantly speed upthis identification process. Clearly, the ability to culture cells incontrolled environments is crucial to this venture so that the benefitsof human genome sequencing can be realized.

[0007] The ability to control the environment is also important in thearea of new drug validation. Bioprocesses associated with new drugs arepermitted a window of operating parameters, e.g., temperature, pH, etc.,that are based on data obtained during the FDA approval process, whereinit has been demonstrated that the new drug is unaltered within thatoperating window. During production of the new drug, any deviation fromthe operating window results in the discarding of that batch of drug.Thus, a technique that permits more data to be generated by conductingexperiments with wider parameter variation and thus, a wider operatingwindow, could be a significant economic benefit to companies whichcurrently have to discard batches of drugs.

[0008] Currently, for bioprocess development and optimization in thepharmaceutical industry, significant numbers of fermentations are neededunder varying environmental and nutritional conditions. This isexpensive and time-consuming in practice, as this type of research istypically performed in shake flasks (with practically no control of thebioprocess parameters) or in 1- to 100-liter laboratory scalebioreactors (Tholudur, A. et al, Biotechnol. Bioeng. 66: 1-16 (1999)).To decrease the number of experiments required for optimization,mathematical modeling is used (Alvarez-Ramirez, J. et al, J. Chem.Technol. Biotechnol 74: 78-84 (1999); Boon, M. A. et al., BiotechnolBioeng. 64: 558- 567 (1999); Cooney, M. J. et al., Biotechnol. Prog. 15:898-910 (1999); Tholudur A. et al., Biotechnol. Bioeng. 66: 1-16(1999)). However, this approach also requires a significant number offermentations for establishing process parameters. Further, currentlyavailable laboratory scale bioreactors are expensive and bulky, thusmaking bioprocess development and optimization inefficient as largenumbers of simultaneous experiments cannot be conducted.

[0009] To overcome the bulky aspect of scale bioreactors, miniaturizedbioreactors have been used (Walther, I. et al., Engine and MicrobialTechnol. 27: 778-783 (2000)). However, in small volumes, e.g., 1-2 ml orless, it is difficult, if not impossible, to use standard industrialprobes for culture monitoring due to the probes' physical dimensions.Another problem is that standard Clark-type oxygen probes consume oxygen(Lee, Y. H. and Tsao, G. T., Advances in Biochemical Engineering, Ghose,T. K. et al. (eds.), Berlin, Springer-Verlag, p. 35 (1979); Bambot, S.B. et al., Biotech. Bioeng. 43: 1139-1145 (1994)). In small volumes,such probes compete with the cells for oxygen which distorts the resultsfrom the bioprocess. In addition, over time, drifts in calibration canoccur (Bambot, S. B. et al., Biotech. Bioeng. 43: 1139-1145 (1994)).Miniaturized versions of standard industry probes are known (Liu, C. C.and Neuman, M. R., Diabetes Care 5: 275-277 (1982); Suzuki, H. et al.,Biosens. Bioelectron. 6: 395-400 (1991); Zhong, L. et al., Chin. J.Biotechnol. 8: 57-65 (1992)). However, their use in bioprocessing is noteconomically feasible due to the sophisticated and expensive techniquesrequired to manufacture the miniaturized probes. Thus, a fast, reliableand inexpensive bioprocessing system and technique, wherein experimentscan be performed, optionally in parallel, in small or large volumes,with on-line measurement and control of multiple process parameters, isstrongly desirable.

SUMMARY OF THE INVENTION

[0010] The present invention combines bioprocessing with opticalchemical sensing technology to monitor, measure, control and/or adjustand thus, to optimize multiple bioprocess parameters in single and/ormultiple bioreactors.

[0011] In one embodiment, the invention is directed to a method ofmonitoring, measuring, controlling and/or adjusting and thus, optimizingat least two cultivation parameters in a cell culture, comprising:

[0012] (a) establishing at least one cell culture in at least onebioreactor, wherein each bioreactor comprises at least two opticalchemical sensors;

[0013] (b) exciting the optical chemical sensors to generate emissionand/or light absorption;

[0014] (c) detecting the emission and/or absorption obtained in (b);

[0015] (d) analyzing the detected emission and/or absorption obtained in(c) to determine the status of the cultivation parameters.

[0016] In another embodiment, the invention is directed to a method ofmonitoring, measuring, controlling and/or adjusting and thus, optimizingat least two cultivation parameters in at least two cell cultures,comprising:

[0017] (a) establishing at least one cell culture in at least twobioreactors in parallel, wherein each bioreactor comprises at least twooptical chemical sensors;

[0018] (b) exciting the optical chemical sensors to generate emissionand/or light absorption;

[0019] (c) detecting the emission and/or absorption obtained in (b);

[0020] (d) analyzing the detected emission and/or absorption obtained in(c) to determine the status of the cultivation parameters.

[0021] In another embodiment, the invention is directed to abioprocessing system, comprising:

[0022] (a) at least one bioreactor;

[0023] (b) at least two optical chemical sensors associated with eachbioreactor, wherein the optical chemical sensors are located within eachbioreactor;

[0024] (c) at least one excitation source corresponding to each opticalchemical sensor; and

[0025] (d) at least one detector.

[0026] An object of the invention is to solve at least the aboveproblems and/or disadvantages and to provide at least the advantagesdescribed hereinafter.

[0027] Additional advantages, objects and features of the invention willbe set forth in part in the description which follows and in part willbecome apparent to those having ordinary skill in the art uponexamination of the following or may be learned from practice of theinvention. The objects and advantages of the invention may be realizedand attained as particularly pointed out in the appended claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[0028] The accompanying drawings, which are incorporated in and form apart of the specification, illustrate exemplary embodiments of thepresent invention and, together with the description, serve to explainthe principles of the invention. In the drawings:

[0029]FIG. 1 is a schematic diagram of a high throughputmicrobioprocessing system in accordance with one embodiment of thepresent invention. In this embodiment, each well of a 96-well microtiterplate can be independently monitored for OD (optical density), pH and DO(dissolved oxygen) and independently controlled for pH and DO.

[0030]FIG. 2 is a schematic diagram of a microbioreactor in accordancewith one embodiment of the present invention. In this embodiment, at theleft cuvette wall, a blue LED (light emitting diode) and an UV LED,together with a 530 nm photodetector, are used to measure pH; at theright cuvette wall, a blue LED and a 590 nm photodetector are used tomeasure DO; a red LED and a 600 nm photodetector are used to measure ODthrough the front and back walls. The air supply inlet and outlet arepositioned at the corners of the cuvette.

[0031] FIGS. 3(a) and 3(b) are schematic diagrams illustrating (a) anoptical configuration of a pH channel; and (b) an optical configurationof an oxygen sensing channel. LED—light emitting diode; APD—avalanchephotodiode; E×F—excitation filter; EmF—emission filter.

[0032] FIGS. 4(a)-4(c) are graphs illustrating three measured parametersduring parallel fermentations of E. coli in a microbioreactor and a1-liter fermentor. Time profiles comparing (a) pH (the circles in thebeginning and end represent the pH values measured with a standard pHmeter); (b) DO; and (c) OD (the circles in the beginning and endrepresent the values measured with a spectrophotometer after dilution)are illustrated.

[0033]FIG. 5 illustrates a commercially available integratedspectrometer and diode array detector containing a self-focusingreflection grating (d=0.2 μm, g=2 μm), an optical fiber for light input,a reflecting edge for light output and a diode array.

[0034]FIG. 6 is a schematic diagram of a single well of a multi-wellplate illustrating an arrangement of optical elements and a pH reagentdispenser in accordance with one embodiment of the present invention.This particular arrangement permits movement of the plate in the x-yplane to enable each well to be monitored and to control pH.

[0035]FIG. 7 is a schematic diagram of a microbioprocessing system inaccordance with one embodiment of the present invention wherein acid,base and nutrient are added to the bioreactors through an instrumenttower connected to a liquid addition arm connected to liquid additiontubes.

[0036]FIG. 8 is a schematic diagram of a microbioreactor in accordancewith one embodiment of the present invention wherein the chemicalsensors are located within the bioreactor and the chemical sensingelectronics are located in a sub-platform. OD is measured via a lightpipe and gas is added via a sparge tube.

[0037]FIG. 9 is a schematic diagram of a bioreactor platform containingreceptacles for 24 microbioreactors in accordance with one embodiment ofthe present invention wherein a pad-type heating element and thermowellsare also present.

[0038]FIG. 10 is a schematic diagram of a sub-platform in accordancewith one embodiment of the present invention wherein bioreactor platformand agitator mounting holes are present.

[0039]FIG. 11 is a schematic diagram of an agitator in accordance withone embodiment of the present invention wherein the agitator isconnected to a sub-platform and mounting plate of a positioning table.

[0040]FIG. 12 is a photograph of a commercially available positioningtable.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

[0041] A key requirement for any bioprocess is the ability to measureand control process parameters. In addition, if one is culturing cells,another key requirement is the ability to supply chemicals such asnutrients, oxygen and pH correctors, to the culture. The presentinvention meets these requirements and overcomes the disadvantages ofknown bioprocessing techniques by using non-invasive optical chemicalsensing technology (Bambot, S. B. et al., Biotechnol. Bioeng. 43:1139-1145 (1994); Randers-Eichhorn, L. et al., Biotechnol. Bioeng. 55:921-926 (1997); Xu, Z. et al, J. Biomed. Mater. Res. 39: 9-15 (1998)) tomonitor, measure, control and/or adjust and thus, to optimize multiplebioprocess parameters in single and/or multiple bioreactors.

[0042] The inventive bioprocessing system and technique removes a majorbottleneck in bioprocess development and allows for much speedier andefficient optimization of bioprocesses such as fermentation. Inaddition, it could dramatically improve microbial isolation andcultivation of new species, as an enormous number of experimentalconditions could be tested on a massively parallel scale.

[0043] Bioprocessing System

[0044] The inventive bioprocessing system (and technique) relies onoptical chemical sensing technology wherein an excitation sourceproduces light which excites an optical chemical sensor to generateemission and/or cause absorption. The emission and/or absorption ismeasured by a detector. The luminescence emitted from the chemicalsensor or the amount of light absorbed by the chemical sensor is relatedto the concentration of an analyte, such as oxygen. If the luminescenceemitted changes, or if the amount of light absorbed changes, then theconcentration of the analyte has changed.

[0045] Since optical chemical sensing technology is employed in theinventive bioprocessing system, the following components must beincluded in the system: a bioreactor, chemical sensor, excitation (orlight) source and detector. These elements are described in detailbelow. To conduct parallel bioprocessing, the system must contain atleast two bioreactors each containing at least one chemical sensor. Tomeasure multiple parameters, at least two chemical sensors must bepresent in each bioreactor (single or multiple bioreactors).

[0046] Optional components in the system are illustrated in FIGS. 7-12and include the following:

[0047] Bioreactor Platform—the bioreactor platform, preferably amachined, anodized, aluminum plate, can function as a bioreactor holder.For example, the bioreactor platform could be used to hold culture vials(exemplary bioreactors) which cannot stand on their own. See, e.g., FIG.7 and FIG. 9 (wherein the bioreactor platform has dimensions of about7.5″ by 5 and ⅜″). The bioreactor platform may be equipped with locatorholes for light pipes and sparge tubes for each bioreactor. The locatorholes keep the pipes and tubes fixed with respect to each bioreactorduring agitation. In addition, the bioreactor platform can be equippedwith thermowells to sense temperature. The bioreactor platform can bemounted to a sub-platform, described below, using mounting holes asillustrated in FIG. 10. If present, these two components function as ashaker mechanism for agitation control.

[0048] Sub-platform—the sub-platform houses the chemical sensors and anyassociated circuitry, such as signal conditioning and multiplexingcomponents, wires harnessed to sensing electronics, etc., for eachbioreactor. The sub-platform is preferably machined, made of aluminumand provided with an anodized finish. It can serve as a holder for thePCB (prototype circuit board) on which the optical components andelectronics can be mounted. A clear, scratch-resistant insert can act asa stop for bioreactors such as culture vials, and as a window for theexcitation sources and detectors. Alternate embodiments of asub-platform are shown in FIG. 7 and FIG. 10 (wherein dimensions areindicated as about 9.5″ by 7 and ⅜″). In a preferred embodiment, thesub-platform extends, on all sides, approximately one inch beyond thebioreactor platform, if present. This extension allows for mounting toan agitator for controlled agitation of the bioreactorplatform/sub-platform assembly.

[0049] Cabling from the optical components and other electroniccomponents (if such cabling is present), can be run in cable troughs toconnectors mounted on one side of the sub-platform. From there, cabling(suitably strain-relieved) can run to the instrument housing, if present(described below).

[0050] Agitator—an agitator provides variable agitation, which ispreferably selected using a software program, for example. See, e.g.,FIG. 7. Agitation rate is preferably not uniform for each bioreactor.However, a uniform agitation rate can be readily employed. If amulti-well plate is used as a bioreactor, then it may be necessary toprovide some means of agitating the plate so as to maintain sufficientdissolved oxygen levels within each bioreactor well. Alternatively, oradditionally, dissolved oxygen levels can be maintained by sparging airat a fixed rate into the medium in each bioreactor.

[0051] A variety of commercial agitators, such as shaker tables, areavailable, such as those manufactured by New Brunswick Scientific Co.,Inc. and Innova LifeSciences Corp. However, commercial tables areusually designed for standalone operation with loads substantiallyhigher than that expected from a bioreactor platform and sub-platform,for example, and they incorporate heavy cast-iron mechanisms designed tominimize travel when placed on a countertop or similar surface. Inaddition, because they are designed to work with large vessels, theirorbital radii are generally greater than that which can be toleratedwithout resulting in splash-over from the bioreactor in the inventivesystem. For these reasons, a simple custom design can be employed in theinventive system incorporating a trio of small offset cams. See, e.g.,FIGS. 10 and 11. One of these cams coupled to a variable speed DC motoris shown schematically in FIG. 11 connected to a mounting plate on apositioning table, described below. A 3 mm offset is indicated in FIG.11. The motor minimizes overall height while providing orbital rates upto about 400 rpm.

[0052] The DC motor can be controlled by a commercially available motorcontrol such as that manufactured by Dart Controls, Inc. The setpoint ofthe controller (displayed on a computer screen as 0-100% full scale) canbe established by a computer based on manual operator entry or can beset automatically based on DO or K₁a. The 100% endpoint can be fixed toachieve a nominal orbital rate of about 350 rpm. Higher rates may createa funneling effect in the bioreactor which can skew DO measurements.

[0053] Alternatively, a simpler means of agitation, such as vibration,rocking, etc., could be employed. If vibrational agitation is selected,then control can be accomplished as described above for orbitalagitation, except that the setpoint limits must be chosen to avoidsplashing (instead of funneling).

[0054] Positioning Table—a desirable positioning table has precise x-yaxis control for the position of individual bioreactors, e.g.,microtiter wells, under a robotic liquid addition arm, if present. See,e.g., FIG. 7. Although a number of x-y-z axis devices exist commercially(such as the DaVinci XYZ system by Techno-isel), they tend to providemore capabilities along the z-axis than is required for the inventivebioprocessing system. As a result, they tend to have a greater heightthan might otherwise be required and do not readily lend themselves toinclusion of an agitator. Therefore, an x-y axis device, such as theUniSlide® by Velmex, Inc. shown in FIG. 12, is preferred. Byincorporating a pair of linear, low profile slides, suitable travel(such as 6″×9″) can be achieved with minimum height (approximately 5.5″)and foot print (approximately 23″×26″ work envelope).

[0055] The positioning table may be provided with motors for positioning(rather than scanning) applications, e.g., with stepper motors and highprecision lead screws. Outboard limit switches may also be provided. Acustom top plate or mounting plate can be coupled via shock mounts tothe shaker assembly, if present, to minimize vibrational transfer to thepositioning table. Commercial controls, programmable as a Windows®application using an RS-232 port, for example, are available and may beutilized as a sub-component of the positioning table. Alternatively,custom control, using an analog or digital position indication systemwith stepper motor controls, may be used.

[0056] Liquid Addition Arm—the liquid addition arm can be used to addchemicals, such as acid, base, nutrient(s), etc., to the bioreactors, asillustrated in FIGS. 1, 6 and 7. The liquid addition arm may be capableof z-axis motion to allow liquid dispensers to be positioned preciselyabove any given bioreactor, e.g., microtiter well. Thus, the chemicalscan be dispensed into the culture medium, for example, to achieve moreprecise volume control and to avoid drop formation problems. A dualelement syringe pump can be used to dispense the requisite chemical(s)to the bioreactors. The pump is a commercial device which can operateunder computer control, and which can be housed in the instrumenthousing, if present. Alternatively, commercial micropipetters can beused, however, such devices add to the overall system height, which is amajor consideration for a system designed to operate under a hood. Inaddition, the liquid addition arm may serve a second purpose -positioning a probe for pH measurements if the skilled artisan does notuse optical pH sensors as described below. Thus, in addition toincorporating the outputs from the pump, if present, the liquid additionarm could also house a pH probe, if required. The liquid addition armitself can be fixed to the x-y positioning table base plate, if present.A constant speed drive with limit switch and precision lead screw, or“pull”-type solenoid with spring return, can be used to provide themeans of arm travel.

[0057] Air Manifold—the air manifold allows for the control of air (atan operator selected flow rate) to sparge elements in each bioreactor.See, e.g., FIG. 8. Flow rates to each bioreactor are preferablyidentical. Flow rate to the manifold can be manually set by the operatorusing, for example, a needle valve and flowmeter or a similar mechanism.Selecting and establishing flow rates are well-within the purview of theskilled artisan. Manifold inlet air supply may be filtered using amembrane filter such as an ACRO 50 0.2 μm PTFE filter.

[0058] Instrument Housing—the instrument housing contains liquidaddition pumps, air system components, sensing electronics, motordrives, positioning controls, etc., if present. The housing can beinterfaced to both the bioreactor platform, if present, and the controland acquisition computer (described below), if present. The housing ispreferably a NEMA rated enclosure affixed to a base plate.

[0059] Computer-Based Data Acquisition and Control System—the dataacquisition and control system is, preferably, a computer-based systemusing data acquisition and control cards, manufactured by MeasurementComputing Corp. of Massachusetts, for example. See, e.g., FIGS. 1 and 7.Such cards can be plug and play and auto-calibrating, without switchesor jumpers, to facilitate replacement in the event of board failure.

[0060] Analog input channels in the data acquisition and control systempreferably have 12-bit resolution with sampling rates up to about 330kHz. Analog inputs can be software selected to function as single-endedor differential inputs, and input channel ranges can be softwareselectable as bipolar or unipolar from about 1.25 to about 10 V.Sampling in burst mode can be provided to minimize channel-to-channelskew by clocking the A/D at the maximum rate between successivechannels. Signal conditioning can be provided for temperature inputswith a nominal half degree Celsius accuracy.

[0061] Analog outputs for use with external controllers, agitatormotors, positioning tables, etc., if present, are preferably 12-bit andhave discrete software selectable ranges. Parallel digital I/O can besoftware selectable as input or output at byte or half-byte levels.Installation, calibration and testing software can be provided by thevendor for system management and testing.

[0062] Regarding software, commercially available software can beemployed such as data acquisition cards, as described above, andgraphical programs including, but not limited to, SoftWIRE®, LabVIEW®,etc. SoftWIRE® is a Visual Basic® based graphical programming languageoffered by Measurement Computing Corp. SoftWIRE® is menu-driven, highlyintuitive and self-documenting. The software utilizes high-level controland graphical user interface (GUI) blocks that are compatible with allof Measurement Computing Corp.'s data acquisition and control cards.Because it is a Visual Basic® extension, it is readily interfaced to anyother custom Visual Basic® application that might be required.

[0063] LabVIEW® is a software/hardware system that provides exceptionalflexibility and one that has been used to control fermentations at the1-liter and above scale. In addition, LabVIEW® provides mathematicaloperations that enable functions such as on-line growth and oxygenuptake rate calculations from real-time OD and DO data, if present.

[0064] The control, acquisition and GUI should be designed for a highdegree of automation as well as system flexibility. In addition toperforming the required control functions, it should permit: operatorentry of system configuration data such as acid and base concentrations;operator configuration of bioreactors (individually or in blocks)including the ability to disable bioreactors as needed; control of theliquid addition arm, if present; control of the positioning tablepositions and movements, if present; operator entry of setpoints andcontrol parameters; means of storing and retrieving previously storedconfigurations; operator selection of scan rates for DO levels, pH,etc.; logging of data to a disk after each measurement cycle or aftermultiple measurement cycles as specified by the operator; graphing ofdata as selected by operator from a variety of formats; alarming ofabnormal conditions as per operator selection; and executing auxiliaryfunctions such as calibration, homing, manual pump selection, etc. Thus,the data acquisition and control system can be used to monitor andcontrol the bioreactors and to log parameters, including, but notlimited to, temperature and agitation rates, for each bioreactor and/orthe bioprocessing system as a whole.

[0065] Bioprocessing and Cell Cultivation

[0066] Monitoring, measuring, controlling and/or adjusting multipleparameters at one time allows the skilled artisan to efficiently andcost-effectively determine optimal conditions for a given cell typeand/or cell environment. By combining cell cultivation with opticalchemical sensing technology, cultivation can be successfully and rapidlyperformed, controlled and monitored in small volumes in an automated,parallel fashion at less expense than current bioprocess techniques. Forexample, a system wherein a plurality of bioprocesses, such asmicrobioprocesses, are conducted in a multi-well microtiter plate (asshown in FIG. 1), can be run for less than the cost of one benchtopbioreactor. Further, plate readers, found in nearly every cultivationlaboratory, offer the opportunity for relatively inexpensive studies ofthe results of parallel bioprocesses (Li, J. et al, Biotech. Bioeng. 70:187-196 (2000)). Thus, additional equipment may not be needed.

[0067] The bioreactor is preferably a cultivation vessel. It can be aslarge as a 1-, 3- or even 100-liter bioreactor or as small as a 100 μlwell on a multi-well microtiter plate, or even as small as microchip, oranywhere in between. The size of the cultivation vessel will depend uponthe experimental parameters, e.g., number of cell types, number ofmedia, number of different conditions to test, etc. The skilled artisancan readily determine the appropriate cell cultivation vessel to employ.For example, if the skilled artisan has twelve different sets ofconditions to determine growth optimization for a particular cell line,then a 12-well plate could be employed. Other cultivation vesselpossibilities include, but are not limited to, cuvettes, culture platessuch as 6-well plates, 24-well plates, 48-well plates and 96-wellplates, culture dishes, microchips, 1-liter or larger bioreactors, cellculture flasks, roller bottles, culture tubes, culture vials, e.g., 3, 4or 5 ml vials, flexible bags, etc. Thus, any type of container can beused as a cultivation vessel.

[0068] Depending upon their configuration within the well-plate, thewells on a well plate can function as microbioreactors or asreceptacles, wherein a culture vessel such as a culture vial is placedin the receptacle and the culture vial becomes the bioreactor and thewell plate becomes a bioreactor platform. Thus, in one embodiment, abioprocessing system is employed wherein, for example, a machined,anodized, aluminum bioreactor platform contains receptacles fortwenty-four 5 ml thick-walled, glass shell culture vials, as illustratedin FIG. 9. The culture vials are flat-bottomed vessels with a diameterand height of approximately 20 mm and each functions as a bioreactor.The vials are spaced on 35 mm centers.

[0069]FIG. 2 illustrates another embodiment wherein a cuvette functionsas a microbioreactor.

[0070] A single well from a multi-well plate, as seen in FIG. 6, is anexample of another bioreactor, more specifically, a microbioreactor. Asmall operating volume of about 100 μl to about 250 μl is possible insuch a bioreactor. See, e.g., FIG. 1 wherein each well in a 96-wellmicrotiter plate functions as a microbioreactor containing approximately250 μl cell-containing nutrient medium. Ideally, such a microbioreactorachieves a K₁a approaching about 70 to about 100 hr⁻¹, which iscomparable to a typical 1-liter laboratory fermentor run at about 700 toabout 800 rpm at about 1 vvm (volume per volume per minute) aeration.

[0071] The cells undergoing cultivation are not limited to a particularcell type. In other words, the inventive bioreactor can be used tocultivate mammalian cells, insect cells, yeast, fungi, bacteria,protozoa, algae, plant cells, etc. Multiple cell types may be cultivatedin parallel in different culture vessels or even in the same culturevessel, e.g., multi-well plate, so long as efforts are made to avoidcross-contamination.

[0072] The culture medium or media employed will depend upon theparticular cell type(s) being cultivated. Determining the appropriateculture medium or media is well-within the purview of the skilledartisan. In the event that different culture media are being tested foroptimization studies, then it would remain well-within the purview ofthe skilled artisan to determine which media to test based on the knownbasic nutrient requirements of the cell type(s). The K₁a of the cultureshould be established to allow for cultivation without encounteringoxygen limitations.

[0073] The culture parameters that can be monitored, measured and/oradjusted and thus, optimized, include, but are not limited to, pH,dissolved oxygen (DO), carbon dioxide level, temperature, glucoseconcentration, phosphate concentration, ammonia concentration, lactateconcentration, metal ion(s) concentration(s), additional nutrientconcentrations, flow rate, pressure, etc. Such parameters can bemonitored continuously. Additionally, OD (optical density) can bemonitored and measured.

[0074] Establishing controlled conditions is well-within the purview ofthe skilled artisan. For example, fermentations can be carried out in ahumidified and temperature controlled oven placed in a sterileenvironment, such as a laminar flow hood to avoid contamination, orunder similarly controlled conditions. Moreover, DO control can becarried out using a stirrer at the bottom of the bioreactor. See, e.g.,FIG. 2. Alternatively, DO control can be carried out using an agitatorthat gently shakes, for example, an entire multi-well plate to allow formaximal oxygen mass transfer through the surface as described above. Ina multi-well plate, the use of an agitator will cause all of the wellsto have the same K₁a, thus allowing for meaningful comparisons to bemade between experiments on a single plate. The agitation rate and theairflow rate combined determine a bioprocessing system K₁a. However, onecould easily run multiple multi-well plates, for example, at differentagitation settings to obtain a broad range of K₁as. Alternatively,individual wells of a multi-well plate, for example, can beindependently agitated using a microelectromechanical system (NEMS)thereby permitting independent DO control of each well. The control andactuation can be implemented using LabVIEW®, for example, or similarsystem. DO control can be accomplished by controlling agitation ratesand/or sparge flow rates to maintain desired average DO levels in abioprocessing system containing multiple bioreactors, or, alternatively,to maintain minimum DO levels in single bioreactors. Software PID(proportional, integral, derivative) loops can be employed for thispurpose.

[0075] pH control can be achieved by means of computer controlledaddition of acid and/or base, i.e., pH correctors, to maintain pH arounda chosen setpoint. In the present invention, precision syringe-pumps canbe used to dispense quantities, including microliter quantities, of 1MHCl or NaOH as described above. A suitable degree of hysteresis may benecessary to prevent overcompensating through excessive liquid additionalthough the skilled artisan can have some flexibility in controllingthe volumes of liquid that need to be added to adequately control pH.

[0076] Results from the continual monitoring can be employed as afeedback mechanism for adjusting the culture parameters. For example,feedback control of pH would be similar to that in lab fermentorswherein acid/base addition is initiated upon deviation from thesetpoint.

[0077] Optical Chemical Sensing

[0078] There are five basic optical chemical sensing techniques:measuring absorbance, fluorescence intensity, ratiometric fluorescence,fluorescence lifetime and fluorescence polarization. Culture parameterssuch as pH and DO can be measured using any of the five techniques,however, the preferred technique is fluorescence lifetime. OD ismeasured via absorbance. Fluorescence lifetime is relatively immune toleaching, photobleaching, excitation light intensity and other artifactswhich may affect fluorescence measurements. In fluorescence lifetime, asuitable quenching lumiphore is excited with modulated light and thelifetime (average time between absorption of a proton and the resultantfluorescence emission) is measured by determining the phase shiftbetween the excitation light and the emission.

[0079] Excitation Source

[0080] As noted above, the excitation source produces light whichexcites the optical chemical sensor. The excitation source employed ispreferably a light-emitting diode (LED) that emits light at a wavelengththat corresponds to the excitation wavelength of the chemical sensor.For example, a blue LED and an UV LED are preferably used to measure pHwhen using a chemical sensor such as a 530 nm photodetector. A blue LEDcan also be used to measure DO when using a 590 nm photodetector. A redLED can be used to measure OD (a chemical sensor is not required tomeasure OD). If a multiple bioreactors are employed, then the skilledartisan could employ as many LEDs as there are bioreactors, as they areinexpensive. Alternatively, other excitation sources known in the art,e.g., laser diodes, can be used to illuminate the chemical sensor. Apass filter or excitation filter may be optionally positioned betweeneach excitation source and its respective chemical sensor to blockwavelengths other than those needed to excite the chemical sensor.

[0081] Detector

[0082] The detector employed to detect the luminescence emitted from orlight absorbed by the optical chemical sensor can be a photodetector,spectrometer and/or diode array, photomultiplier tube (PMT), chargecoupled device (CCD) camera, semiconductor photoreceiver or otherdetector known in the art. The design wavelength of the detector used ispreferably matched to the luminescence wavelength of the respectivechemical sensor. For example, if photodetectors are employed, then a 530nm photodetector can be used to measure the luminescence from a pHchemical sensor, a 590 nm photodetector can be used to measure theluminescence from a DO chemical sensor and a 600 nm photodetector can beused to measure OD. A pass filter or emission filter may be optionallypositioned between each chemical sensor and its respective detector toblock wavelengths other than the luminescence wavelength of the chemicalsensor.

[0083] Detection of bioprocess parameters can occur in numerous ways,depending upon the multiplexing of excitation sources and detectors.Multiplexing allows electronics to be shared by several chemicalsensors. The combination of excitation sources and detectors will dependupon the system limitations, size of the bioreactor(s), cost and amountof space available.

[0084] For example, if the excitation source is an LED and if thedetector can only detect emission over a limited wavelength range, e.g.,a photodetector, then the following combinations could be employed:

[0085] provide at least one LED for each parameter being measured (via arespective chemical sensor) and provide at least one photodetector foreach chemical sensor corresponding to the emission wavelength of therespective chemical sensor, wherein the LEDs and photodetectors movefrom bioreactor to bioreactor using a simple robot; or

[0086] provide at least one LED for each parameter being measured (via arespective chemical sensor) for each bioreactor and provide, for eachbioreactor, one photodetector for each chemical sensor corresponding tothe emission wavelength of the respective chemical sensor.

[0087] If the excitation source is an LED and if the detector cananalyze multiple wavelengths, then detection can occur via opticalfibers coupled to a single diode array, for example. Specifically, oneor more optical fibers can be used to couple the light emitted from thechemical sensors in each bioreactor to the diode array. For example, thefibers from each bioreactor in a multi-well plate can be brought to thedetector and each bioreactor can be independently illuminated with anLED for the necessary excitation of the chemical sensor(s). This permitsall the fibers to be coupled to the detector such that the data fromeach well is reported only when that well is illuminated. If necessary,an integrating sphere (a highly reflective surface, an example of whichis shown in FIG. 1) can be positioned under each bioreactor to increasethe light collection efficiency. Using this technique, each bioreactorcan be read successively, as illustrated in FIG. 1. Thus, the followingcombinations could be employed:

[0088] provide at least one LED for each parameter being measured (via arespective chemical sensor), wherein the LEDs move from bioreactor tobioreactor using a simple robot, as illustrated in FIG. 1, or provide awide area electroluminescent display for each parameter measured (via arespective chemical sensor), and provide one spectrometer for resolvingthe wavelengths of light emitted from the various chemical sensors; or

[0089] provide at least one LED for each parameter being measured (via arespective chemical sensor) for each bioreactor and provide onespectrometer for each bioreactor.

[0090] An advantage of using a larger bioreactor, such as a cuvette, isthat conventional optics employing photodetectors, for example, can beused which results in increased signal levels as substantially all theexcitation light is coupled to the chemical sensors. An advantage ofusing a smaller bioreactor, such as a well on a microtiter plate, isthat optical fibers can be used. When optical fibers are employed, anintegrated spectrometer/detector capable of 2-3 nm resolution, forexample, can be used. Such an integrated device is illustrated in FIG.5, and is available from Microvision, Inc., Bothell, Wash. Use of thisdevice eliminates the need for emission filters and thus, providescomplete spectral information, which simplifies ratiometric measurementsand provides additional flexibility in eliminating potential opticalinterferences.

[0091] Another embodiment is an arrangement wherein each bioreactortravels past a sensor head containing an LED and detector, positioned asillustrated in FIG. 2 for the single cuvette-based prototype. FIGS. 6and 8 show possible arrangements of sensors for a single bioreactor in amulti-well plate. In FIG. 6, the pH and DO are read off the bottom ofthe well while the OD LED, e.g., red LED, rides along with the pHreagent dispenser above the well. The bottom of the well contains pH andoxygen sensor patches which are activated using blue and UV LEDs,respectively. A lens is used to maximize collected light emitted fromthe chemical sensors and direct it to the detector. In FIG. 8, DO and pHsensors are located in a sub-platform directly below the bottom of thewell and OD is measured via a light pipe. These three arrangements wouldallow for the use of a positioning table, e.g., x-y platform, to movethe multi-well plate.

[0092] Chemical Sensors

[0093] The number, types and sizes of optical chemical sensors employedcan vary depending upon the chosen bioreactors. For example, thephysical dimensions of the chemical sensors can be large for use with 1-to 100-liter bioreactors, or can be very small, e.g., optical fibers,for use with a microtiter well or microchip. Since optical chemicalsensors are typically based on equilibrium principles, their presence ina cell culture will typically not interfere with cultivation. In otherwords, the chemical sensors are non-invasive.

[0094] Chemical sensors include, but are not limited to, fluorescentdyes added directly to the bioreactor medium, sensor “patches” appliedto at least one wall of the bioreactor, sensing films applied to atleast one wall of the bioreactor and any other optical chemical sensorknown in the art. “Sensing films” and “sensor patches” areinterchangeable phrases. The phrase “bioreactor walls” is intended tomean the sides, top and/or bottom of the bioreactor. Chemical sensorpatches preferably comprise luminescent compounds immobilized in apolymeric membrane. Immobilization allows for maximum response, sensorreuse and minimal interference. If sensor patches are employed, they canbe placed inside the bioreactor as illustrated in FIGS. 1, 2, 3(b) and6, for example. Alternatively, as there is no need for physical contactwith the detector, the chemical sensors can be sealed and sterilized.

[0095] The chemical sensor can be attached to the bioreactor wall using,for example, silicone grease. The grease prevents the chemical sensorfrom peeling off the wall and penetrating the medium between the sensorand the detector. As another alternative, the chemical sensor can becovered, by a layer of black silicone for optical isolation from thefermentation medium, or the wall(s) of the bioreactor can be coveredwith black tape (with a window for exposing the chemical sensor toexcitation light) to prevent excitation of the medium by the excitationlight. These various alternatives can be practiced individually or incombination.

[0096] Since some of the components (especially the filters, if present)may be bigger than the bioreactor walls, e.g., cuvette walls, attentionmust be paid to the proper spatial placement of the optical componentsaround the bioreactor to avoid optical crosstalk between the channels.Exemplary positioning of the basic components for pH and DO channels isshown in FIGS. 3(a) and 3(b), respectively.

[0097] pH

[0098] Chemical sensors used to measure pH include any known ratiometricpH sensitive dye, such as 1-hydroxypyrene-3,5,7-sulfonic acid (HPTS). Asterilized solution of the dye can be directly introduced into thebioreactor medium and detected via fluorescence. Fluorescence detectioncan be determined using front face geometry (FIG. 3(a)). For example,HPTS has two excitation peaks—400 and 450 nm. When excited at either 400or 450 nm, HPTS will emit light at approximately 520 nm. The longerexcitation peak can be excited using a blue LED (460 nm), for example,and the shorter excitation peak can be excited using an UV LED (375 nm),for example. The intensity ratio of the 520 nm fluorescence emissionsfrom excitation at each of the two excitation peaks is affected by thepH of the medium. Thus, the pH can be calibrated by measuring theintensity ratio of the 520 nm fluorescence emissions at each of the twoexcitation peaks as the pH changes. pH can be optionally verified on abenchtop pH meter. This ratiometric approach avoids interference fromturbidity changes and provides accurate measurements of pH.

[0099] One possible problem with HPTS is the range of the emissionspectrum since its emission maximum is 520 nm. To overcome this problem,the skilled artisan could employ green fluorescent protein (GFP). GFP isa pH sensitive dye which possesses a very similar emission spectrum toHPTS, but it emits at longer wavelengths. GFP can be used with an UV ora blue LED as the excitation source, depending upon background levelsand the required sensitivity and selectivity (Kostov, Y. et al.,Biotechnol. Bioeng. 70: 473-477 (2000)).

[0100] Another possibility is to measure pH using a nonradiative energytransfer system based on a sensing film wherein a ruthenium-based dye,for exampleruthenium(II)-tris-(4,4′-diphenyl-2,2′-bipyridyl)-trimethylsilylpropansulfonate,functions as a luminescent donor, and a pH-sensitive dye, such asbromothylmolblue, functions as an acceptor. The sensing film is createdby mixing the two dyes with a polymer, such as polyurethane, andapplying it to a transparent support, such as polystyrene, using, forexample, an ethanol-based solvent (Liebsch, G. I. et al, Appl.Spectroscopy 54: 548-559 (2000)).

[0101] Another possibility for measuring pH is to use an immobilizedindicator dye. In fact, although it is not necessary, it is preferablefor the indicator dye to be immobilized as long as it does not interferewith cell growth. Sol-gel chemistry and ethyl cellulose films have beensuccessfully used to immobilize pH indicators (Bambot, S. B. et al.,Sensors and Actuators B (Chemica) 22: 181-188 (1995); Chang, Q. et al.,Biotechno. Prog. 14: 326-331 (1998)). Epoxy resins may also work well asimmobilization matrices.

[0102] A non-sensor based alternative can also be used if the bioreactorsize is sufficient wherein a dip probe incorporating an ion selectiveFET (field effect transistor) is employed. Such a probe can be mountedon the end of the liquid addition arm, if present.

[0103] Oxygen

[0104] DO sensors include, but are not limited to, ruthenium-basedoxygen sensing films such as Ru(II) tris(4,7-diphenyl-1,10-phenanthroline) complex, immobilized in a siliconerubber membrane (Bambot, S. B. et al, Biotechnol Bioeng. 43: 1139-1145(1994)). An exemplary optical configuration of the DO components isshown in FIG. 3(b) wherein black silicone film is attached to thebioreactor wall using silicone grease. In FIG. 3(b), a wall of thebioreactor is covered with black tape (with a window for the chemicalsensor) to prevent excitation of the medium by the excitation source.

[0105] As an alternative, DO can be measured using a chemical sensorwherein an indicator dye such as a porphyrin dye, for example ametalloporphyrin such as platinum(II)-octaethylporphyrin, is combinedwith, e.g., encapsulated within, a polymer matrix such as polystyrene.The matrix layer is then applied to a polystyrene support using, forexample a toluene-based solvent (Liebsch, G. I. et al., Appl.Spectroscopy 54: 548-559 (2000)).

[0106] As an alternative, ratiometric oxygen measurement based on a newclass of compounds that show dual emission peaks, an oxygen insensitiveand an oxygen sensitive one, can be employed. Such compounds include,but are not limited to, heterocyclic-substituted platinum1,2-enedithiolates such as BPh₄ ((dppe)Pt{S₂C₂(CH₂CH₂—N-2-pyridinium)},wherein “dppe” is 1,2-bis(diphenylphosphino)ethane) (Kostov, Y. et al.,Appl. Spectroscopy 54: 864-868 (2000)). By measuring the ratio of thetwo emission peaks, the skilled artisan can quantify the ambient oxygentension around the chemical sensor (Kostov, Y. and Rao, G., Rev. Sci.Inst. 70: 4466-4470 (1999)). An advantage of this technique is that itwould allow the same circuitry to be employed for both DO and pHmeasurements. Another advantage of this technique is that it providescontinuous calibration.

[0107] In all cases described above, DO is measured using luminescentquenching. Although, as noted above, dual emission compounds can be usedin a ratiometric measurement system as well. In luminescent quenching,DO is detected using frequency domain detection of ruthenium orporphyrin fluorophore lifetime, for example, wherein the excitationlight is modulated and the lifetime is measured by determining the phaseshift between the modulated excitation light and the resulting modulatedfluorescence emission. This is a well-established method of oxygendetection (Bambot, S. B. et al, Biotechnol. Bioeng. 43: 1139-1145(1994)) and relies on the reversible quenching of fluorescence emissiondue to oxygen binding. Its greatest advantage is that the measurementsare equilibrium based and do not consume oxygen.

[0108] DO calibration can be achieved using an air-nitrogen blendingsetup, for example, and recording the phase shift going from nitrogen toair. Thus, a simple calibration procedure will suffice, such as a singlepoint calibration at 100% DO in a gas.

[0109] Temperature

[0110] Temperature can be measured using thermal deactivation techniqueswhich employ, for example, dyes such as ruthenium-based dyes, forexample ruthenium(II)-tris-(1,10-phenanthroline)-hexafluorophosphate, ona polymer matrix such as poly(acrylo-nitrile) using adi-methylformamide-containing solvent (Liebsch, G. I. et al., Appl.Spectroscopy 54: 548-559 (2000)). The polymer matrix prevents thequenching of the ruthenium complex by oxygen.

[0111] Alternatively, temperature can be measured using fluorescentprobes that respond to temperature such that even individual bioreactor,e.g., well, temperature control can be obtained in a multi-well plate(Liebsch, G. I. et al., Appl. Spectroscopy 54: 548-559 (2000)) when theprobes are combined with resistance-based heating.

[0112] Alternatively, temperature can be measured by thermistors orother sensing devices placed in thermowells, as illustrated in FIG. 9.Such devices can be wired through a data acquisition card to permitcomputer display, logging and control. Redundant readings can beaveraged to determine the temperature.

[0113] If a bioprocessing system is employed wherein a bioreactorplatform is present, then temperature can be measured and controlled viathe bioreactor platform which can act as a heating element as it can beequipped with four thermowells for temperature sensing. See, e.g., FIGS.7 and 9. For example, if the bioreactor is housed in a receptacle in abioreactor platform, then a pad-type heating element, such as Chromalox®or its equivalent, can be sized so as to raise the top surface of thebioreactor platform from ambient temperature to a temperature of, forexample, about 40 degrees C., within a period of, for example, about 15to about 20 minutes. The pad-type heating element's power supply can bemodulated in ON/OFF fashion by a computer controlled relay, so as toemulate a PID temperature controller. The pad-type heating element canbe fabricated with holes to match those in the sub-platform, if present.

[0114] The bioreactor platform can be sized so that the combination ofbioreactor platform and pad-type heating element has a thicknessapproximately equal to the height of each bioreactor. For example, ifthe bioreactors are culture vials, then the height of the bioreactorplatform and pad-type heating element would be approximately equal tothe culture vial height. If additional heating is needed for adequatetemperature control, then the sub-platform, if present, can befabricated as two layers with an additional heater between the layers.This decreases the temperature gradient across the bioreactor platformand allows for separately controlled “heating zones.” If additionalheating is needed, the overall height of the bioreactor system shouldstill be equal to the height of the bioreactors.

[0115] Carbon Dioxide

[0116] Nonradiative energy transfer can be used to measure carbondioxide levels. For example, indicator dye combinations such as aruthenium-based dye, for exampleruthenium(II)-tris-(4,4′-diphenyl-2,2′-bipyridyl)-trimethylsilylpropansulfonateand m-cresolpurple wherein the former is the donor and the latter is theacceptor, can function effectively to measure carbon dioxide presence(or absence) and changes thereof (Liebsch, G. I. et al, Appl.Spectroscopy 54: 548-559 (2000)). The two dyes can be added to an ethylcellulose matrix using a toluene- and ethanol-containing solvent andthen added to a polyester support.

[0117] Optical Density

[0118] The OD of the cell suspension in the medium can be directlymeasured using an LED that emits at approximately 600 nm, for example.Specifically, a yellow LED (595 nm) attached to each bioreactor's lightpipe, if present, can be driven by a current source modulated at apredetermined frequency, thereby modulating the output light at the samepredetermined frequency. The modulated light passes through the lightguide, which is held in the medium a fixed distance from the bottom ofthe bioreactor, and is detected by a photodetector (which can beequipped with a 600 nm bandpass filter, if desired) mounted beneath thebottom of the bioreactor. Lock-in detection can be used to detect onlylight that is modulated at the predetermined frequency, thereby removingnoise and the effects of ambient light (which is not modulated) from thesignal. A calibration procedure for OD can be provided similar to thatfor DO, allowing the measurement of light at each photodetector prior tothe addition of liquid to the associated bioreactor.

[0119] Alternatively, OD can be measured using conventional equipmentsuch as a plate reader, or using microbore column chromatography or flowinjection analysis.

[0120] Additional Applications

[0121] Apart from the obvious utility of allowing much speedierbioprocess development and optimization, the inventive bioprocessingsystem could open the way to discovering new species of microorganisms.The currently available strains are believed to be a small fraction ofthe total species. Since many microorganisms are thought to be simplyuncultivable in a laboratory setting, an approach where an enormousnumber of culture conditions can be tried may target the optimalcombination necessary for culturing novel microbes.

[0122] In addition, the inventive bioprocessing system is not limited tocell cultivation. For example, one skilled in the art could conductenzymatic and other biological reactions in parallel to optimizeconditions, determine parameters and/or conduct comparison studies. Byinterfacing with a fast analysis system such as capillaryelectrophoresis or perfusion chromatography, the inventive bioprocessingsystem could be automated even more such that product profiles are alsoavailable.

[0123] The invention is illustrated by the following example which isnot intended to be limiting.

EXAMPLE 1

[0124] In this example, the working volume was scaled down to about 2 mlby using a disposable cuvette as the bioreactor. The design of themicrobioreactor is presented in FIG. 2. Three parameters, pH, DO and OD,were continuously measured using optical chemical sensors. A testfermentation was performed in the microbioreactor and the results werecompared with the results from a fermentation in a standard 1 literbioreactor.

[0125] The working bioreactor was a disposable polystyrene cuvette, 1×1cm, with a total volume of 4 ml. To avoid contamination duringcultivation, it was equipped with a silicone rubber cap. The cap had aninlet for air delivery and outlet for exhaust air. The inlet and outletwere positioned at the corners of the cuvette to avoid overlapping withthe optical path for OD measurements. The inlet was connected to an airsparger, as indicated in FIG. 2, which was fabricated from a 100 μlplastic pipette tip. Three tubes with inner diameters of 0.25 mm werepositioned at the end of the tip. The tubes were glued using epoxyresin. The outlet consisted of a short piece of a 16-gauge syringeneedle. The air was supplied by an aquarium pump, passed through aregulator for low gas flow rate and filtered using a syringe filter(Millex®-GV, 0.22 μm, Millipore, Bedford, Mass.). Stirring was executedby a small magnetic stir bar and magnetic stirrer. The K₁a of thecuvette was adjusted to be approximately equal to the K₁a of a 1-literfermentor operated at 300 rpm agitation and 1 vvm aeration (21 h⁻¹).

[0126] The cuvette was large enough to accommodate conventional opticsand electronics and thus, no optical fibers were needed. Solid statelight sources, e.g., LEDs, and detectors, and low-cost optical filtersand electronics were used. As some of the components (especially thefilters) were bigger than the cuvette wall, attention was paid to theproper spatial placement of the optical components around the cuvette inorder to avoid crosstalk between the channels. The positioning of thebasic components for the pH and DO channels is shown in FIGS. 3(a) and3(b), respectively.

[0127] The pH measurements were performed using the ratiometric pHsensitive dye 1-hydroxypyrene-3,5,7-sulfonic acid, (HPTS, Sigma, St.Louis, Mo.), pKa=7.2, a non-toxic indicator, used for blood gasmeasurements in vivo (Zhang, S. et al., Med. Biol Eng. Comput. 33:152-156 (1995)). The 7.2 pKa makes HPTS appropriate for use withneutral-range bioprocesses. A sterilized solution of HPTS was directlyintroduced into the culture media. Its addition to the media did notinfluence cell growth.

[0128] The absorbency of the cell suspension was directly measured usinga 600 nm LED. For this particular setup, the maximum OD detected wasapproximately 9 (results not shown).

[0129] The DO channel was positioned on the opposite wall of the cuvetteto the pH channel using the ruthenium-based oxygen sensorRu(diphenylphenanthroline)₃ ²⁺, immobilized in silicone rubber (Bambot,S. B. et al., Biotechnol. Bioeng. 43: 1139-1145 (1994)). The opticalconfiguration of the components is shown in FIG. 3(b). The sensing filmwas attached to the cuvette wall using silicone grease (high vacuumgrease, Dow Corning, Midland, Mich.). The sensing film was covered by alayer of black silicone (GE 312A, General Electric Company, Waterford,N.Y.) for optical isolation from the fermentation medium. The wall ofthe cuvette was covered with black tape (with a window for the chemicalsensor) to prevent excitation of the medium.

[0130] Oxygen detection was performed using frequency domain detectionof ruthenium fluorophore lifetime, wherein the excitation light wasmodulated and the lifetime was measured by determining the phase shiftbetween excitation light and fluorescence emission (Bambot, S. B. etal., Biotechnol Bioeng. 43: 1139-1145 (1994)). Calibration was achievedby using an air-nitrogen blending set-up and recording the phase shiftgoing from nitrogen to air.

[0131] The performance of the microbioreactor was tested by conductingparallel fermentations of E. coli in the cuvette and a 1-liter BIOFLO™III New Brunswick Scientific Co., Inc.) fermentor. Both were inoculatedat the same time from the same seed culture after setting them to rununder identical K₁as (the fermentor was run at 300 rpm and 1 vvmaeration (21 hr⁻¹)). The K₁a was arbitrarily chosen asagitation/aeration above this level led to foaming in themicrobioreactor which was clearly caused by the ad hoc fabrication ofthe aeration system and an inefficient magnetic stir-bar which served asthe agitator. Comparisons of the resulting profiles are shown in FIGS.4(a)-4(c).

[0132] As can be seen, the profiles of pH, DO and OD are very similar inboth processes. The patterns of oxygen depletion during the exponentialgrowth as well as the recovery of DO to 100% at the end of the processare similar in both cases. The correlation coefficient between the OD ofthe two fermentations was 0.984, indicating very similar growth profilesin the two cultures. However, all the specific points of themicrobioreactor process occurred approximately 2 hours earlier.Additional investigation showed that after about 1 hour, themicrobioreactor heated up approximately 3° C. above the ambienttemperature due to Joule heating (the cuvette was not equipped fortemperature control). Thus, while the cells in the 1-liter bioreactorwere cultivated at 25° C., the microbioreactor cells were cultivated at28° C. Taking into account that the optimal temperature for E. coli is37° C., the temperature elevation may explain the slightly increasedcell growth rate and decreased lag time in the microbioreactor. Onesolution to the problem would be the use of a small thermoelectricdevice for temperature control.

[0133] To ensure that pH and OD measurements did not affect each other,their values were verified by offline measurements in the beginning andthe end of the process. The results are shown in the respective figures(FIGS. 4(a) and 4(c)). Offline pH and OD values agreed very well withthe online values and demonstrated stability over the period ofoperation, i.e., no drift.

[0134] This example demonstrates that a bioprocess can be successfullyperformed in small volumes (about 2 ml in this example). The use ofsemiconductor excitation sources and detectors in this design makes fora very compact and low-cost detection system.

[0135] The foregoing embodiments and advantages are merely exemplary andare not to be construed as limiting the present invention. Thedescription of the present invention is intended to be illustrative andis not intended to limit the scope of the claims. Many alternatives,modifications and variations will be apparent to those skilled in theart. In the claims, means-plus-function clauses are intended to coverthe structures described herein as performing the recited function andnot only structural equivalents, but also equivalent structures.

[0136] The above cited references, including any and all articles areincorporated by reference herein where appropriate for appropriateteachings of additional or alternative details, features and/ortechnical background.

What is claimed is:
 1. A bioprocessing system, comprising: (a) at leastone bioreactor; (b) at least two optical chemical sensors associatedwith each bioreactor, wherein the optical chemical sensors are locatedwithin each bioreactor; (c) at least one excitation source correspondingto each optical chemical sensor; and (d) at least one detector.
 2. Thebioprocessing system of claim 1, wherein each bioreactor is a wellhoused in a multiple-well plate.
 3. The bioprocessing system of claim 2,wherein the optical chemical sensors are sensor patches positioned atthe bottom of the well.
 4. The bioprocessing system of claim 1, whereineach bioreactor is a cuvette.
 5. The bioprocessing system of claim 4,wherein the optical chemical sensors are sensor patches affixed to atleast one wall of the cuvette.
 6. The bioprocessing system of claim 1,wherein each bioreactor is a culture vial housed within a receptacle ofa multi-receptacle bioreactor platform.
 7. The bioprocessing system ofclaim 6, wherein the optical chemical sensors are sensor patchespositioned at the bottom of the culture vial.
 8. The bioprocessingsystem of claim 7, wherein the excitation source is a light emittingdiode.
 9. The bioprocessing system of claim 8, wherein the detector isan integrated spectrometer and diode array.
 10. The bioprocessing systemof claim 1, further comprising a bioreactor platform containing at leastone receptacle to house each bioreactor.
 11. The bioprocessing system ofclaim 10, further comprising a sub-platform, wherein the bioreactorplatform is positioned on top of the sub-platform.
 12. The bioprocessingsystem of claim 11, further comprising an agitator, wherein thesub-platform is positioned on top of the agitator.
 13. The bioprocessingsystem of claim 12, further comprising a positioning table, wherein thepositioning table is positioned below the agitator such that thepositioning table is capable of moving the bioreactor in an x-y or x-y-zplane to a predetermined position.
 14. The bioprocessing system of claim1 or 13, further comprising a data acquisition and control systemconnected to components of the bioprocessing system via cabling means.